Statistical Genomics Group - Publications

 

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Research Papers - Peer reviewed (Journals)

  1. Liu, J. and C. Sabatti (2000) "Generalized Gibbs sampler and multigrid Monte Carlo for Bayesian computation," Biometrika 87: 353-369. Preprint
  2. Bressman, S., C. Sabatti, D. Raymond, D. de Leon, C. Klein, P. L. Kramer, M. F. Brin, S. Fahn, X. Breakefield, L. J. Ozelius, and N. J. Risch (2000) "The DYT1 phenotype and guidelines for diagnostic testing," Neurology 54: 1746-1752.
  3. Liu, J., C. Sabatti, J. Teng, B. Keats, and N. Risch (2001) "Bayesian analysis of haplotypes for linkage disequilibrium mapping," Genome Research 11: 1716-24. Preprint
  4. Pastinen, T., I. Jaakko, M. Perola, C. Sabatti, P. Tainola, M.Levander, A. Syvanen, and L. Peltonen (2001) "Dissecting a population genome for targeted screening of disease mutations," Human Molecular Genetics 10: 2961-2972.
  5. Sabatti, C., S. Karsten, and D. Geschwind (2002) "Thresholding rules for recovering a sparse signal from microarray experiments," Mathematical Biosciences 176: 17-34. Preprint
  6. Karsten, S., V. Van Deerlin, C. Sabatti, L. Gill, and D. Geschwind (2002) "An evaluation of TSA signal amplification and archived fixed and frozen tissue in microarray gene expression analysis," Nucleic Acid Research (NAR methods online) 30: e4.
  7. Sabatti, C. and N. Risch (2002) "Homozygosity and linkage disequilibrium," Genetics 160: 1707-1719. Preprint
  8. Sabatti, C. (2002) "Measuring dependence with volume tests," The American Statistician 50: 191-195. Preprint
  9. Sabatti, C., L. Rohlin, M. Oh, and J. Liao. (2002) "Co-expression pattern from DNA microarray experiments as a tool for operon prediction," Nucleic Acid Research 30: 2886-2893. Reprint
  10. Jen, J., C. Coulin, T. Bosley, M. Salih, C. Sabatti, S. Nelson, and R. Baloh (2002) "Familial horizontal gaze palsy with progressive scoliosis maps to chromosome 11q23-25," Neurology 59: 432-435.
  11. Sabatti, C. and K. Lange (2002) "Genomewide motif identification using a dictionary model," IEEE Proceedings 90: 1803-1810. Preprint
  12. Sabatti, C., S. Service, and N. Freimer (2003) "False discovery rates in linkage and association linkage genome screens for complex disorders," Genetics 164: 829-833. Reprint
  13. Karsten, S., L. Kudo, R. Jackson, C. Sabatti, H. Kornblum, and D. Geschwind (2003) "Global analysis of gene expression in neural progenitors reveals specific cell-cycle and metabolic networks," Developmental Biology 261: 165-182.
  14. Liao, J., R. Boscolo, Y. Yang, L. Tran, C. Sabatti, and V. Roychowdhury (2003) "Network component analysis: reconstruction of regulatory signals in biological systems," Proceedings of the National Academy of Science 100: 15522-15527. Reprint
  15. Kao, K., Y. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury, and J. Liao (2004) "Determination of multiple transcription regulator activities in Escherichia coli using network component analysis," Proceedings of the National Academy of Science 101: 641-646. Reprint
  16. Lee, H., H. Wang, J.C. Jen, C. Sabatti, R.W. Baloh, and S.F. Nelson (2004) "A novel mutation in KCNA1 causes episodic ataxia without myokymia," Human Mutation 24: 536.
  17. Jen, J. C., H. Wang, H. Lee, C. Sabatti, R. Trent, I. Hannigan, K. Brantberg, G. M. Halmagyi, S. F. Nelson, and R. W. Baloh (2004) "Suggestive linkage to chromosome 6q in families with bilateral vestibulopathy," Neurology 63: 2376-2379.
  18. Sabatti, C., L. Rohlin, K. Lange, and J. Liao (2005) "Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites," Bioinformatics 21: 922-931.
  19. Boscolo, R., C. Sabatti, J. Liao, and V. Roychowdhury (2005) "A generalized framework for network component analysis", IEEE Transaction in Computational Biology and Bioinformatics, 2:289-301.
  20. Erickson, S. and C. Sabatti (2005) "Empirical Bayes estimation of a sparse vector of gene expression," Statistical Applications in Genetics and Molecular Biology, 4 :22.
  21. Wang, H., Y. Lee, S. Nelson, and C. Sabatti (2005) "Inferring genomic loss and location of tumor suppressor genes from high density genotypes," UCLA Stat preprint 423, Journal of the French Statistical Society, 146: 153-171
  22. Riley, R., C. Lee, C. Sabatti, and D. Eisenberg (2005) "Measuring evidence for protein domain interactions from multi-species protein interaction data," Genome Biology 6: R89.
  23. Falcon-Perez, J., R. Nazarian, C. Sabatti, and E. Dell'Angelica (2005) "Distribution and dynamics of Lamp1-containing endocytic organelles in fibroblasts deficient in biogenesis of lysosome-related organelles complex-3 (BLOC-3)," Journal of Cell Science 118: 5243-5255.
  24. Sabatti, C. and G. James (2006) "Bayesian sparse hidden components analysis for transcription regulation networks," Bioinformatics, 22 : 739-746.
  25. Ayers, K., C. Sabatti, and K. Lange (2006) "Reconstructing ancestral haplotypes with a dictionary model," Journal of Computational Biology, 3, 3: 767-785.
  26. Service, S., J. De Young, H. Pretorious, J. Roos, M. Karayiorgou, G. Bedoya, J. Ospina, A. Ruiz Linares, A. Macedo, J. Palha, P. Heutink, Y. Aulchenko, B. Oostra, C. van Duijn, M. Jarvelin, T. Varilo, L. Peltonen, L. Peddle, P. Rahman, G. Piras, M. Monne, S. Murray, L. Galver, C. Sabatti, A. Collins, N. Freimer (2006) "Extent, distribution and magnitude of linkage disequilibrium in eleven population isolates," Nature Genetics, 38, 556-560.
  27. Lee, H. J. Jen, H. Wang, Z. Chen, H. Mamsa, C. Sabatti, R. Baloh, and S. Nelson (2005), "A genome-wide linkage scan of familial benign recurrent vertigo: linkage to 22q12 with evidence of heterogeneity" Hum. Mol. Genet., 15: 251-258.
  28. Herzberg,I., A. Jasinska, J. Garcia, D. Jawaheer, S. Service, B. Kremeyer, C. Duque, M. Parra, J. Vega, D. Ortiz, L. Carvajal, G. Polanco, G. Restrepo, C. Lopez, C. Palacio, M. Levinson, I. Aldana, C. Mathews, P. Davanzo, J. Molina, E. Fournier, J. Bejarano, M. Ramirez, C. Ortiz, X. Araya, C. Sabatti, V. Reus, G. Macaya, G. Bedoya, J. Ospina, N. Freimer, and A. Ruiz-Linares (2006) "Convergent linkage evidence from two Latin-American population isolates supports the presence of a susceptibility locus for bipolar disorder in 5q31-34," Human Molecular Genetics 15: 3146-3153.
  29. Keen-Kim, D., C. Mathews, V. Reus, T. Lowe, L. Herrera, C. Budman, V. Gross-Tsur, A. Pulver, R. Bruun, G. Erenberg, A. Naarden, C. Sabatti, N. Freimer (2006) "Overrepresentation of rare variants in a specific ethnic group may confuse interpretation of association analyses," Human Molecular Genetics 15: 3324-3328.
  30. Service, S., J. Molina, J. Deyoung, D. Jawaheer, I. Aldana, T. Vu, J. Bejarano, E. Fournier, M. Ramirez, C. Mathews, P. Davanzo, G. Macaya, L. Sandkuijl, C. Sabatti, V. Reus, N. Freimer (2006) "Results of a SNP genome screen in a large Costa Rican pedigree segregating for severe bipolar disorder," Am J Med Genet B Neuropsychiatr Genet. 141: 367-73.
  31. Wang, H., C. Lin, S. Service, The international collaborative group on isolated populations, Y. Chen, N. Freimer, C. Sabatti (2006) "Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density," Human Heredity , 62 : 175-189.
  32. Chen, Y., C. Lin, C. Sabatti (2006) "Volume measures for linkage disequilibrium," BMC Genetics 7:54
  33. Ayers, K., C. Sabatti and K. Lange (2007) "A dictionary model for haplotyping, genotype calling, and association mapping," Genetic Epidemiology 31 : 672-683.
  34. Cha, Y., J. Brodsky, G. Ishiyama, C. Sabatti, and R. Baloh (2006) "The relevance of migraine in patients with Meniere's disease" Acta Oto-laryngologica 127 : 1241-1245.
  35. Service, S., The international collaborative group on isolated populations, C. Sabatti, N. Freimer (2007) "Tag SNPs chosen from HapMap perform well in several population isolates," Genetic Epidemiology, 31 : 189-194.
  36. Cha, Y.H., J. Brodsky, G. Ishiyama, C. Sabatti, R. Baloh (2008) "Clinical features and associated syndromes of mal de debarquement," J Neurol, 255: 1038-44.
  37. Sabatti, C. and K. Lange (2008) "Bayesian Gaussian mixture models for high density genotyping arrays," JASA 103 : 89-100. preprint
  38. Stefansson, H. et al (2008) Large recurrent microdeletions associated with schizophrenia, Nature 455 232-6.
  39. Vrijenhoek, T., J. Buizer-Voskamp, I. van der Stelt, E. Strengman, Genetic Risk and Outcome in Psychosis (GROUP) Consortium, C. Sabatti, A. van Kessel, H. Brunner, R. Ophoff, J. Veltman (2008) "Recurrent CNVs Disrupt Three Candidate Genes in Schizophrenia Patients," The American Journal of Human Genetics, 83: 504-510.
  40. Sabatti. C., S. Service, A. Hartikainen, A. Pouta, S. Ripatti, J. Brodsky, C. Jones, N. Zaitlen, T. Varilo, M. Kaakinen, U. Sovio, A. Ruokonen, J. Laitinen, E. Jakkula, C. Lachlan, C. Hoggart, P. Elliott, A. Collins, H. Turunen, S. Gabriel, M. McCarthy, M. Daly, M-R. Jarvelin, N. Freimer, L. Peltonen (2009) "Genomewide association analysis of metabolic phenotypes in a birth cohort from a founder population," Nature Genetics, 41: 35-46.
  41. Rujescu D, Ingason A, Cichon S, Pietilainen OP, Barnes MR, Toulopoulou T, Picchioni M, Vassos E, Ettinger U, Bramon E, Murray R, Ruggeri M, Tosato S, Bonetto C, Steinberg S, Sigurdsson E, Sigmundsson T, Petursson H, Gylfason A, Olason PI, Hardarsson G, Jonsdottir GA, Gustafsson O, Fossdal R, Giegling I, Moller HJ, Hartmann AM, Hoffmann P, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Djurovic S, Melle I, Andreassen OA, Hansen T, Werge T, Kiemeney LA, Franke B, Veltman J, Buizer-Voskamp JE; GROUP Investigators, Sabatti C, Ophoff RA, Rietschel M, Nothen MM, Stefansson K, Peltonen L, St Clair D, Stefansson H, Collier DA (2009) "Disruption of the neurexin 1 gene is associated with schizophrenia," Hum Mol Genet, 18: 988-96.
  42. H. Wang, Veldink,J., R. Ophoff, C. Sabatti (2008) "Markov models for inferring Copy Number Variations from genotype data on Illumina platforms," UCLA Statistics Preprint #533 and Human Heredity, 68: 1-22.
  43. Jasinska, A., S. Service, D. Jawaheer, J. DeYoung, M. Levinson, Z. Zhang, B. Kremeyer, H. Muller, I. Aldana, J. Garcia, G. Restrepo, C. Lopez, C. Palacio, C. Duque, M. Parra, J. Vega, D. Ortiz, G. Bedoya, C. Mathews, P. Davanzo, E. Fournier, J. Bejarano, M. Ramirez, C. Araya Ortiz, X. Araya, J. Molina, C. Sabatti, V. Reus, J. Ospina, G. Macaya, A. Ruiz-Linares, and N.B. Freimer (2009) "Narrow and Highly Significant Linkage Signal for Severe Bipolar Disorder in the Chromosome 5q33 Region in Latin American Pedigrees," Am J Med Gen Part B, 150: 998-1006.
  44. Hattori, D., Y. Chen, B. Matthews, L. Salwinski, D. Eisenberg, C. Sabatti, W. Grueber, L. Zipuski (2009) "Robust discrimination between self and non-self neurites requires thousands of Dscam1 isoforms," Nature, 461: 644-648.
  45. Ghiani, C., M. Starcevic, I. Rodriguez-Fernandez, R. Nazarian, V. Cheli, L. Chan, J. Malvar, J. de Vellis, C. Sabatti, and E Dell’Angelica (2010) "The dysbindin-containing complex (BLOC-1) in brain: developmental regulation, interaction with SNARE proteins, and role in neurite outgrowth," Molecular Psychiatry, 15: 204-215.
  46. Kang, H., J-H. Sul, S. Service, N. Zaitlen, S.Kong, N. Freimer, C. Sabatti*, E. Eskin* (2010) "Variance component model to account for sample structure in genome-wide association studies," Nature Genetics, 42 : 348-354.
  47. Zhang, Z., K. Lange, R. Ophoff, C. Sabatti (2010) "Reconstructing DNA copy number by penalized estimation and imputation," The Annals of Applied Statistics , 4: 1749-1773
  48. James, G., Sabatti, C., Zhou, N. and Zhu, J. (2010) "Sparse Regulatory Networks," The Annals of Applied Statistics , 4: 663-686.
  49. Teslovich TM et al. (2010) "Biological, clinical and population relevance of 95 loci for blood lipids," Nature 466:707-713.
  50. Pietilainen OP, Rehnstrom K, Jakkula E, Service SK, Congdon E, Tilgmann C, Hartikainen AL, Taanila A, Heikura U, Paunio T, Ripatti S, Jarvelin MR, Isohanni M, Sabatti C, Palotie A, Freimer NB, Peltonen L. (2011) "Phenotype mining in CNV carriers from a population cohort," Hum Mol Genet. 20: 2686-95.
  51. Buizer-Voskamp JE, Muntjewerff JW; Genetic Risk and Outcome in Psychosis (GROUP) Consortium, Strengman E, Sabatti C, Stefansson H, Vorstman JA, Ophoff RA. (2011) "Genome-Wide Analysis Shows Increased Frequency of Copy Number Variation Deletions in Dutch Schizophrenia Patients," Biol Psychiatry 70:655-62.
  52. Visnyei, K., H. Onodera, R. Damoiseaux, K. Saigusa, S. Petrosyan, D. De Vries, D. Ferrari, J. Saxe, E. Panosyan, M. Masterman-Smith, J. Mottahedeh, K. Bradley, J. Huang, C. Sabatti, I. Nakano, H. Kornblum (2011) "A molecular screening approach to identify and characterize inhibitors of glioblastoma multiforme stem cells," Molecular Cancer Therapeutics 10:1818-28.
  53. Zhang, Z., K. Lange and C. Sabatti (2012) "Reconstructing DNA copy number by joint segmentation of multiple sequences" BMC Bioinformatics 13:205.

    Research Papers - Peer reviewed (Conference Proceedings)

  54. Liu, J. and C. Sabatti (1998) "Simulated sintering: Markov chain Monte Carlo with spaces of varying dimensions," Bayesian Statistics, J.M. Bernardo, J.O. Berger, A. P. Dawid, and A.F.M. Smith (eds). New York: Oxford University Press.
  55. Sabatti, C., L. Rohlin, J. Liao (2003) "Dictionary model for the analysis of E. Coli promoter regions," Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 4: 3711-3714.
  56. Sabatti, C. and L. Rohlin (2004) "A Bayesian approach to expression network component analysis," Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society 2: 2933-2936. Preprint

    Chapters

  57. Sabatti, C. (2006) "False discovery rate and multiple comparisons procedures" DNA microarrays and related genomic techniques , Allison, Page, Beasley, and Edwards ed., Chapman & Hall/CRC, pg. 289-304.
  58. Sabatti, C. and K. Lange (2007) "Genomewide motif identification using a dictionary model," Genomics and proteomics engineering in medicine and biology , Metin Akay ed., Wiley and IEEE Press, pg. 157-172.
  59. Sabatti, C. (2007) "Avoiding false discoveries in association studies," Linkage disequilibrium and association mapping: analysis and applications , A. Collins ed., Humana Press, pg.195-211.

    Letters to Editor (peer reviewed)

  60. Sabatti, C. and N. Risch (2003) "Response to the letter "Gametic and zygotic associations" by Rong-Cai Yang," Genetics 165: 451-452.

    Reviews (peer reviewed)

  61. Sabatti, C. (2002) "Statistical Issues in DNA Microarrays," Current Genomics 3: 7-15.
  62. Liao, J. and C. Sabatti (2002) "Gene expression arrays," American Society for Microbiology News 68: 432-437.
  63. Sabatti, C. (2004) "Interplay in the computational analysis of genomic regulatory sequences and microarray expression data" Current Genomics 5: 439-442.

    Editorials (peer reviewed)

  64. Freimer, N. and C. Sabatti (2003) "The human phenome project," Nature Genetics 34: 15-21. Reprint
  65. Freimer, N. and C. Sabatti (2004) "Pedigree, sib-pair, and association studies of common diseases; genetic mapping and epidemiology," Nature Genetics 36: 1045-1051. Reprint
  66. Freimer, N. and C. Sabatti (2005) "Guidelines for association studies in Human Molecular Genetics," Human Molecular Genetics, 14: 2481-2483.
  67. Sabatti, C. (2005) "Comment on the "Semilinear high-dimensional model for normalization of microarray data: a theoretical analysis and partial consistency" by Fang et al.," Journal of the American Statistical Association, 100: 796-799.
  68. Sabatti, C. (2006) "Comment on the `Likelihood-Based Inference on haplotype effects in genetic association studies' by Lin and Zeng," Journal of the American Statistical Association 101: 104-106. (Invited contribution.)
  69. Freimer, N. and C. Sabatti (2007) "Human genetics: variants in common diseases." Nature 445: 828-30. (Invited contribution.)

    Unpublished manuscripts and technical reports

  70. Sabatti, C. (1998) "Group Transformations and Dimensionality Reduction in Transition Rules for MCMC," Ph.D. Thesis, Statistics Department, Stanford University.
  71. Sabatti, C., K. Visnyei, H. Kornblum (2008) "Statistical challenges in High-throughput Screens." UCLA Stat Preprint 532
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